(9/7/05) The following is a list of programs on the Web that I find useful for analyzing DNA and designing cloning strategies.

Primer3: I've found this to be a simple way to identify primer pairs for PCR amplification.  Its particularly useful for identifying a pair of primers for cloning PCR fragments because you can set the sequence of one primer or constrain the region in which one or both primers are sought. 

IDT SciTools: We buy most of our oligos from IDT.  This link provides a primer selection program that I've not used - I use Primer3.  I use OligoAnalyzer 3.0 at the IDT site to make certain primer combinations are not likely to form homo- or hetero-dimers.

NEBcutter v2.0: This program identifies restriction sites and open reading frames.  I've found it very useful for designing cloning strategies that require the fusion of two open reading frames.  The program allows you to do a BLAST analysis on any of the open reading frames.  This is useful for identifying the proteins in the clone and for locating junctions between fusion proteins.

Local Alignment Tool: This program aligns matching sequences.  I like it because it retains the numbering of bases used in a DNA strider file so I can easily go back and forth.  Its useful when trying to align real sequence results with a sequence in strider or for locating where an oligo makes a complete or partial match to another sequence.

FlyBase: This is your entry to a wealth of information for working with Drosophila.